Natural selection that affected modern humans early in their evolution has likely shaped some of the traits that set present-day humans apart from their closest extinct and living relatives. The ability to detect ancient natural selection in the human genome could provide insights into the molecular basis for these human-specific traits. Here, we introduce a method for detecting ancient selective sweeps by scanning for extended genomic regions where our closest extinct relatives, Neandertals and Denisovans, fall outside of the present-day human variation. Regions that are unusually long indicate the presence of lineages that reached fixation in the human population faster than expected under neutral evolution. Using simulations, we show that the method is able to detect ancient events of positive selection and that it can differentiate those from background selection. Applying our method to the 1000 Genomes data set, we find evidence for ancient selective sweeps favoring regulatory changes and present a list of genomic regions that are predicted to underlie positively selected human specific traits.

在进化早期影响现代人类的自然选择很可能塑造了一些特征，使当今人类与已灭绝和现存的近亲区别开来。检测人类基因组中古代自然选择的能力可以为了解这些人类特异性特征的分子基础提供见解。在这里，我们介绍了一种通过扫描扩展的基因组区域来检测古代选择性扫描的方法，在这些区域中，我们最近的灭绝亲戚尼安德特人和丹尼索瓦人不属于当今人类的变异范围。异常长的区域表明存在谱系，这些谱系在中性进化下比预期更快地在人群中固定下来。通过模拟，我们表明该方法能够检测古代的正选择事件，并且可以将其与背景选择区分开来。将我们的方法应用于 1000 个基因组数据集，我们找到了古代选择性扫描有利于监管变化的证据，并提出了预计构成积极选择的人类特定性状基础的基因组区域列表。